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Many algae produce triacylglycerides (TAG) when starved for assimilable nitrogen. In the model organism Chlamydomonas reinhardtii , and probably in other species, nitrogen starvation is also the cue to prepare for sexual reproduction. The ensuing process of gametogenesis entails a host of physiological and gene expression changes, which makes it difficult to distinguish the changes that are peculiar to TAG accumulation from other aspects of gametogenesis. As others have found, we show here that the chlorophyte Ettlia oleoabundans produces TAG under conditions of nitrogen deprivation and elevated NaCl concentrations. We exploit these two conditions, and the intermediate response of the organism to intermediate levels of stress, to identify physiological and gene regulatory features in common. Strikingly, TAG levels and chlorophyll concentrations are inversely correlated across both sets of conditions. Similarly, membrane lipids undergo related compositional changes under the two conditions. In contrast, RNA-seq analysis reveals substantially different expression profiles. This is useful because the gene expression changes that are in common, against this background of expression differences, are more likely to be relevant to the shared changes in physiology and lipid composition. Gene expression changes in common include transcripts related to fatty acid synthesis and degradation, TAG synthesis, and a putative TAG lipase that is substantially down-regulated. The identification of properties that are shared by distinct TAG-inducing conditions could facilitate the engineering of algal strains with improved TAG production properties.

Lectins are carbohydrate binding proteins with important roles in many biological processes such as adhesion. Here we have identified 11 potential lectins from Mycobacterium tuberculosis H37Rv genome, using a comprehensive bioinformatics analysis, which will provide helpful clues in molecular mapping of pathogenesis and perhaps also serve as potential drug targets.

Understanding the molecular mechanisms of immunological memory assumes importance in vaccine design. We had earlier hypothesized a mechanism for the maintenance of immunological memory through the operation of a network of idiotypic and anti-idiotypic antibodies (Ab2). Peptides derived from an internal image carrying anti-idiotypic antibody are hypothesized to facilitate the perpetuation of antigen specific T cell memory through similarity in peptide-MHC binding as that of the antigenic peptide. In the present work, the existence of such peptidomimics of the antigen in the Ab2 variable region and their similarity of MHC-I binding was examined by bioinformatics approaches. The analysis employing three known viral antigens and one tumor-associated antigen shows that peptidomimics from Ab2 variable regions have structurally similar MHC-I binding patterns as compared to antigenic peptides, indicating a structural basis for memory perpetuation. (C)) 2007 Elsevier Inc. All rights reserved.

The role of lectins in mediating cancer metastasis, apoptosis as well as various other signaling events has been well established in the past few years. Data on various aspects of the role of lectins in cancer is being accumulated at a rapid pace. The data on lectins available in the literature is so diverse, that it becomes difficult and time-consuming, if not impossible to comprehend the advances in various areas and obtain the maximum benefit. Not only do the lectins vary significantly in their individual functional roles, but they are also diverse in their sequences, structures, binding site architectures, quaternary structures, carbohydrate affinities and specificities as well as their potential applications. An organization of these seemingly independent data into a common framework is essential in order to achieve effective use of all the data towards understanding the roles of different lectins in different aspects of cancer and any resulting applications. An integrated knowledge base (CancerLectinDB) together with appropriate analytical tools has therefore been developed for lectins relevant for any aspect of cancer, by collating and integrating diverse data. This database is unique in terms of providing sequence, structural, and functional annotations for lectins from all known sources in cancer and is expected to be a useful addition to the number of glycan related resources now available to the community. The database has been implemented using MySQL on a Linux platform and web-enabled using Perl-CGI and Java tools. Data for individual lectins pertain to taxonomic, biochemical, domain architecture, molecular sequence and structural details as well as carbohydrate specificities. Extensive links have also been provided for relevant bioinformatics resources and analytical tools. Availability of diverse data integrated into a common framework is expected to be of high value for various studies on lectin cancer biology. CancerLectinDB can be accessed through http://proline.physics.iisc.ernet.in/cancerdb .

Lectins, a class of carbohydrate-binding proteins, are now widely recognized to play a range of crucial roles in many cell-cell recognition events triggering several important cellular processes. They encompass different members that are diverse in their sequences, structures, binding site architectures, quaternary structures, carbohydrate affinities, and specificities as well as their larger biological roles and potential applications. It is not surprising, therefore, that the vast amount of experimental data on lectins available in the literature is so diverse, that it becomes difficult and time consuming, if not impossible to comprehend the advances in various areas and obtain the maximum benefit. To achieve an effective use of all the data toward understanding the function and their possible applications, an organization of these seemingly independent data into a common framework is essential. An integrated knowledge base ( Lectindb, http://nscdb.bic.physics.iisc.ernet.in ) together with appropriate analytical tools has therefore been developed initially for plant lectins by collating and integrating diverse data. The database has been implemented using MySQL on a Linux platform and web-enabled using PERL-CGI and Java tools. Data for each lectin pertain to taxonomic, biochemical, domain architecture, molecular sequence, and structural details as well as carbohydrate and hence blood group specificities. Extensive links have also been provided for relevant bioinformatics resources and analytical tools. Availability of diverse data integrated into a common framework is expected to be of high value not only for basic studies in lectin biology but also for basic studies in pursuing several applications in biotechnology, immunology, and clinical practice, using these molecules.